Mercurial > repos > xuebing > sharplabtool
comparison tools/ilmn_pacbio/quake.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="quake" name="Quake" version="1.0.0"> | |
2 <description>Quality-aware error correction</description> | |
3 <command interpreter="python"> | |
4 quake_wrapper.py --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1 | |
5 </command> | |
6 <inputs> | |
7 <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" /> | |
8 <param name="k" type="integer" value="16" label="Size of k-mers to correct" /> | |
9 </inputs> | |
10 <configfiles> | |
11 <configfile name="fofnfile"> | |
12 ${input1.file_name} | |
13 </configfile> | |
14 </configfiles> | |
15 <outputs> | |
16 <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" /> | |
17 </outputs> | |
18 <help> | |
19 | |
20 **What it does** | |
21 | |
22 Applies the Quake_ algorithm for quality-aware correction of | |
23 substitution error in short reads. | |
24 | |
25 Kelley DR, Schatz MC, Salzberg SL. | |
26 "Quake: quality-aware detection and correction of sequencing errors." | |
27 *Genome Biol.* 2010;11(11):R116. | |
28 | |
29 .. _Quake: http://www.cbcb.umd.edu/software/quake | |
30 | |
31 **Parameter list** | |
32 | |
33 k | |
34 k-mer size for detecting spurious k-mers versus true k-mers from | |
35 the genome. Recommendations for choosing a value of k can be found | |
36 here_. | |
37 | |
38 .. _here: http://www.cbcb.umd.edu/software/quake/faq.html | |
39 | |
40 **Output** | |
41 | |
42 A FASTQ file of corrected and trimmed reads. | |
43 </help> | |
44 </tool> |